This package provides a Go implementation of Kalev and Habeck's HHfrag algorithm from their 2011 paper in Bioinformatics. Notably, this implementation uses hhsuite 2.0 with either hhsearch or hhblits from Johann Soeding in lieu of the older hhsuite 1.5/1.6 version (which requires PSI-BLAST).
http://godoc.org/github.com/TuftsBCB/hhfrag
Once you have Go installed, just run
go get github.com/TuftsBCB/hhfrag
to install the package.